Computational protocol: Shift of fleshy fruited species along elevation: temperature, canopy coverage, phylogeny and origin

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Protocol publication

[…] A phylogenetic tree was constructed for all the seed plants in the communities studied using Phylomatic (version 3) with an APG III derived mega-tree as the base tree. Bladj block in the software Phylocom (version 4.2, available online: was used to assign branch lengths to the obtained tree. For each quadrat, we calculated the phylogenetic index PD, the sum of unique branch lengths of species in the quadrat, which served as a measure of phylogenetic diversity.In order to characterize the relationships between the proportion of fleshy-fruited species in a community and elevation, generalized linear models (GLMs) with Poisson family and log link were fitted, and the total number of species in each individual quadrat was taken as an offset. For each plant community, the following attributes were considered: elevation, number of families (NF), number of genera (NG) and PD (the latter three corrected against total species number). Since these attributes were significantly correlated (r > 0.68, p < 0.05, n = 66), we tested models that included no more than two attributes. In addition to the linear term of elevation, we also considered the square of this variable. In total, 12 models were constructed () and evaluated for each mountain separately and for the entire region. We selected the model with the lowest AICc value and any other model with ∆AICc < 2. Additionally, regression models were used to analyze whether species richness of various growth forms and the whole plants with fleshy fruits were related to elevation, respectively.All the analyses were implemented in R3.1.1. GLMs were built with the function glm within R package stats, and model selection was made with the function aictab within R package AICcmodavg. […]

Pipeline specifications

Software tools Phylomatic, Phylocom
Application Phylogenetics